BELVU(1)
NAME
belvu - View multiple alignments in good-looking colours.
SYNOPSIS
belvu [options] <multiple_alignment>|- [X options]
<multiple_alignment>|- = alignment file or pipe.
DESCRIPTION
Belvu presents multiple sequence alignments in a colourful biologically
interpretable manner.
OPTIONS
-c Print Conservation table.
-l <file> Load color code file.
-L <file> Load Markup color code file.
-m <file> Read file with matching sequence segments.
-r Read alignment in 'raw' format (Name sequence).
-R Do not parse coordinates when reading alignment.
- -o <format> Write alignment or tree to stdout in this format and exit.
- Valid formats: MSF, Mul(Stockholm), Selex,
- FastaAlign, Fasta, tree.
- -n <cutoff> Make non-redundant to <cutoff> %identity at startup.
- -Q <cutoff> Remove columns more gappy than <cutoff>.
- -q <cutoff> Remove sequences more gappy than <cutoff>.
- -P Remove partial sequences at startup.
- -C Don't write coordinates to saved file.
- -z <char>
- Separator char between name and coordinates in saved file.
- -a Show alignment annotations on screen (Stockholm format only).
- -p Output random model probabilites for HMMER.
(Based on all residues.)- -S <order>
- Sort sequences in this order.
- a -> alphabetically o -> by Swissprot organism, alphabetically s -> by score n -> by Neighbor-joining tree u -> by UPGMA tree S -> by similarity to first sequence i -> by identity to first sequence
- -s <file>
- Read in file of scores.
- -T <method> Start up with tree calculated by method:
n -> Neighbor-joining u -> UPGMA N -> Neighbor-joining, only show tree U -> UPGMA, only show tree c -> Don't color tree by organism o -> Don't display sequence coordinates in tree s -> Use Storm & Sonnhammer distance correction r -> Use uncorrected distances- -b <#>
- Print out # bootstrapped trees and exit
- (Negative value -> display bootstrap trees on screen)
- -O <label>
- Read organism info after this label (default OS)
- -t <title>
- Set window title.
- -g Draw grid line (for debugging).
- -u Start up with uncoloured alignment (faster).
- -h Show this help.
- -v Show version info.
Some X options: -acefont <font> Main font. -font <font> Menu font.
SEE ALSO
For documentation, see: http://www.cgb.ki.se/cgb/groups/sonnhammer/Belvu.html
AUTHOR
Erik Sonnhammer <Erik.Sonnhammer@cgb.ki.se>
VERSION
- Version 2.16, compiled Aug 18 2009